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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PCYT1B |
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Phenotypic Information for PCYT1B(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PCYT1B |
Familial Cancer Database: PCYT1B |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PCYT1B |
MedGen: PCYT1B (Human Medical Genetics with Condition) | |
ClinVar: PCYT1B | |
Phenotype | MGI: PCYT1B (International Mouse Phenotyping Consortium) |
PhenomicDB: PCYT1B |
Mutations for PCYT1B |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCYT1B related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AI952718 | PCYT1B | 13 | 287 | X | 24668190 | 24676354 | GALNT1 | 281 | 404 | 18 | 33270975 | 33271098 | |
AI656193 | PCYT1B | 13 | 287 | X | 24668190 | 24676354 | GALNT1 | 281 | 404 | 18 | 33270975 | 33271098 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=39) | (# total SNVs=5) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr23:24597510-24597510 | p.R211C | 3 |
chr23:24608151-24608151 | p.E159K | 2 |
chr23:24625952-24625952 | p.D82N | 2 |
chr23:24608208-24608208 | p.R140C | 2 |
chr23:24608226-24608226 | p.E134K | 2 |
chr23:24608140-24608140 | p.K162N | 1 |
chr23:24665167-24665167 | p.S19F | 1 |
chr23:24580418-24580418 | p.E368Q | 1 |
chr23:24608229-24608229 | p.Y133N | 1 |
chr23:24593350-24593350 | p.N265S | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 3 | 1 | 7 | 1 |   |   |   | 2 |   |   | 6 | 3 |   |   |   | 5 | 3 |   | 4 |
# mutation |   | 3 | 1 | 6 | 1 |   |   |   | 2 |   |   | 6 | 3 |   |   |   | 5 | 3 |   | 5 |
nonsynonymous SNV |   | 3 | 1 | 5 | 1 |   |   |   | 2 |   |   | 4 | 2 |   |   |   | 4 | 2 |   | 4 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 2 | 1 |   |   |   | 1 | 1 |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chrX:24608140 | p.K144N,PCYT1B | 2 |
chrX:24608229 | p.E350G,PCYT1B | 1 |
chrX:24580417 | p.E141K,PCYT1B | 1 |
chrX:24690710 | p.R14C | 1 |
chrX:24597473 | p.E350Q,PCYT1B | 1 |
chrX:24608231 | p.F139S,PCYT1B | 1 |
chrX:24580418 | p.G3G | 1 |
chrX:24690741 | p.S321L,PCYT1B | 1 |
chrX:24597530 | p.L135L,PCYT1B | 1 |
chrX:24608251 | p.S317L,PCYT1B | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for PCYT1B |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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AIPL1,BCL2L14,BYSL,CCDC67,E2F3,ETV6,GPM6B, GPR161,JAKMIP2,NR2E1,P2RX3,PAQR9,PCYT1B,SOHLH2, tAKR,TAS1R1,TET1,TTLL8,UCHL1,USP49,ZNF705D | ARHGAP19,CACNA1C,COL17A1,COL4A5,COL4A6,GRIA4,ITGA2, NEO1,NFASC,PCYT1B,PTPRT,RARB,SDK2,SEMA5A, SEPT3,SHC4,SLC27A6,SRGAP3,SV2A,ZNF561,ZNF648 | ||||
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ATP1B2,BAI3,C14orf132,CEND1,CNTN2,DCAF12L2,GPR88, GRIA1,HMP19,KCNK3,MLLT11,NACAD,PCYT1B,PDZD4, RGAG4,RND2,SALL2,SLC22A17,TAGLN3,TCEAL5,TMEFF2 | ACTG2,ACTN1,AOC3,ATP1A2,BVES,CALD1,CNN1, CTXN1,DACT3,FAM46B,FLNA,RBFOX3,ITGB3,NLGN1, PCYT1B,PDLIM7,PYGM,SGCD,SLC8A2,TAGLN,ZFHX4 |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for PCYT1B |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00122 | phosphate cytidylyltransferase 1, choline, beta | approved; nutraceutical | Choline | ![]() | ![]() |
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Cross referenced IDs for PCYT1B |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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